You can also specify different column labels if you don't want to usethe defaults. Do this by specifying a -labels hash referenceparameter when creating the HSPTableWriter object. The keys of thehash should be the column number (left-most column = 1) for the label(s)you want to specify. Here's an example:

Bio::SearchIO::Writer::HSPTableWriter generates output at the finestlevel of granularity for data within a search result. Data for each HSPwithin each hit in a search result is output in tab-delimited format,one row per HSP.
Here are the columns that can be specified in the -columnsparameter when creating a HSPTableWriter object. If a -columns parameteris not specified, this list, in this order, will be used as the default.

query_name # Sequence identifier of the query. query_length # Full length of the query sequence hit_name # Sequence identifier of the hit hit_length # Full length of the hit sequence round # Round number for hit (PSI-BLAST) rank expect # Expect value for the alignment score # Score for the alignment (e.g., BLAST score) bits # Bit score for the alignment frac_identical_query # fraction of identical substitutions in query frac_identical_hit # fraction of identical substitutions in hit frac_conserved_query # fraction of conserved substitutions in query frac_conserved_hit # fraction of conserved substitutions in hit length_aln_query # Length of the aligned portion of the query sequence length_aln_hit # Length of the aligned portion of the hit sequence gaps_query # Number of gap characters in the aligned query sequence gaps_hit # Number of gap characters in the aligned hit sequence gaps_total # Number of gap characters in the aligned query and hit sequences start_query # Starting coordinate of the aligned portion of the query sequence end_query # Ending coordinate of the aligned portion of the query sequence start_hit # Starting coordinate of the aligned portion of the hit sequence end_hit # Ending coordinate of the aligned portion of the hit sequence strand_query # Strand of the aligned query sequence strand_hit # Strand of the aligned hit sequence frame # Reading frame of the aligned query sequence hit_description # Full description of the hit sequence query_description # Full description of the query sequence frac_identical_total # fraction of total identical substitutions frac_conserved_total # fraction of total conserved substitutions

For more details about these columns, see the documentation for thecorresponding method in Bio::Search::HSP::HSPI.

Title : end_report Usage : $self->end_report() Function: The method to call when ending a report, this is mostly for cleanup for formats which require you to have something at the end of the document. Nothing for a text message. Returns : string Args : none

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